Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study Irene Stefanaki 1 , Orestis A. Panagiotou 2. , Elisavet Kodela 1. , Helen Gogas 3 , Katerina P. Kypreou 1 , Foteini Chatzinasiou 1 , Vasiliki Nikolaou 1 , Michaela Plaka 1 , Iro Kalfa 4 , Christina Antoniou 1 , John P. A. Ioannidis 2,5 , Evangelos Evangelou 2,6 , Alexander J. Stratigos 1 * 1 Department of Dermatology, University of Athens Medical School, Andreas Sygros Hospital, Athens, Greece, 2 Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece, 3 Department of Internal Medicine, University of Athens, Laikon Hospital, Athens, Greece, 4 Blood Donation Unit, Laikon Hospital, Athens, Greece, 5 Stanford Prevention Research Center, Department of Medicine and Department of Health Research and Policy, Stanford University School of Medicine, and Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, California, United States of America, 6 Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom Abstract Background: Genetic association studies have revealed numerous polymorphisms conferring susceptibility to melanoma. We aimed to replicate previously discovered melanoma-associated single-nucleotide polymorphisms (SNPs) in a Greek case- control population, and examine their predictive value. Methods: Based on a field synopsis of genetic variants of melanoma (MelGene), we genotyped 284 patients and 284 controls at 34 melanoma-associated SNPs of which 19 derived from GWAS. We tested each one of the 33 SNPs passing quality control for association with melanoma both with and without accounting for the presence of well-established phenotypic risk factors. We compared the risk allele frequencies between the Greek population and the HapMap CEU sample. Finally, we evaluated the predictive ability of the replicated SNPs. Results: Risk allele frequencies were significantly lower compared to the HapMap CEU for eight SNPs (rs16891982 – SLC45A2, rs12203592 – IRF4, rs258322 – CDK10, rs1805007 – MC1R, rs1805008 - MC1R, rs910873 - PIGU, rs17305573- PIGU, and rs1885120 - MTAP) and higher for one SNP (rs6001027 – PLA2G6) indicating a different profile of genetic susceptibility in the studied population. Previously identified effect estimates modestly correlated with those found in our population (r = 0.72, P,0.0001). The strongest associations were observed for rs401681-T in CLPTM1L (odds ratio [OR] 1.60, 95% CI 1.22– 2.10; P = 0.001), rs16891982-C in SCL45A2 (OR 0.51, 95% CI 0.34–0.76; P = 0.001), and rs1805007-T in MC1R (OR 4.38, 95% CI 2.03–9.43; P = 2 6 10 25 ). Nominally statistically significant associations were seen also for another 5 variants (rs258322-T in CDK10, rs1805005-T in MC1R, rs1885120-C in MYH7B, rs2218220-T in MTAP and rs4911442-G in the ASIP region). The addition of all SNPs with nominal significance to a clinical non-genetic model did not substantially improve melanoma risk prediction (AUC for clinical model 83.3% versus 83.9%, p = 0.66). Conclusion: Overall, our study has validated genetic variants that are likely to contribute to melanoma susceptibility in the Greek population. Citation: Stefanaki I, Panagiotou OA, Kodela E, Gogas H, Kypreou KP, et al. (2013) Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study. PLoS ONE 8(2): e55712. doi:10.1371/journal.pone.0055712 Editor: Sophia N. Karagiannis, King’s College London, United Kingdom Received July 23, 2012; Accepted December 29, 2012; Published February 5, 2013 Copyright: ß 2013 Stefanaki et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The present work was funded by Aristeia Program. This Program is co-funded by the European Social Fund and National Resources (Project code:1094). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: alstrat@hol.gr . These authors contributed equally to this work. Introduction Plethora of studies has shown that ultra-violet (UV) light exposure and certain phenotypic traits, i.e. red or blonde hair, light-colored eyes, fair skin complexion, and prominent mole pattern are major risk factors for the development of cutaneous melanoma (CM) [1–6]. A strong genetic background has been supported by twin studies showing a 55% contribution of genetic effects in melanoma variation liability [7]. High-penetrance germline mutations in CDKN2A and CDK4 genes are rare (0.2–1.2%) in sporadic CM, but they are encountered in approximately 5% of families with only two members with CM, and in 30–40% of families with 3 or more affected members [8–10]. The advent of high-throughput genotyping technologies and their utilization in population-based PLOS ONE | www.plosone.org 1 February 2013 | Volume 8 | Issue 2 | e55712